Merge pull request #7 from mawebster/FSL

Fixed build for FSL6.0.x
ecr05 · Apr 24, 2019 · 7f7410e · 7f7410e
2 parents 44a2f8f + c5805f4
commit 7f7410e
Show file tree

Hide file tree

Showing 3 changed files with 27 additions and 52 deletions.
diff --git a/src/DiscreteOpt/Makefile b/src/DiscreteOpt/Makefile
@@ -2,14 +2,11 @@
 include ${FSLCONFDIR}/default.mk
 
 PROJNAME=DiscreteOpt
-HOCR=True
-USRCXXFLAGS=-g -DNDEBUG  
+USRCXXFLAGS=-g -DNDEBUG
 USRINCFLAGS =-I${INC_NEWMAT} -I${INC_NEWRAN} -I${INC_ZLIB} -I${INC_CPROB} -I${INC_PROB} -I${INC_BOOST} -I${FSLDEVDIR}/include -I${FSLDEVDIR}/extras/include
 USRLDFLAGS =-L${LIB_NEWMAT} -L${LIB_NEWRAN} -L${LIB_ZLIB} -L${LIB_CPROB} -L${LIB_PROB} -L${FSLDEVDIR}/lib #${TBBLIBPATH}
 
-LIBS=-lnewmeshclass -lfslsurface -lgiftiio  -lexpat -lfslvtkio -lnewimage  -lmiscmaths -lfslio -lniftiio -lnewmat -lutils  -lbint -lnewran -lprob -lznz -lz
-MYPROGRAMOBJ=similarities.o DiscreteCostFunction.o  DiscreteModel.o 
-MYPROGRAM=DiscreteOpt
+MYPROGRAMOBJ=similarities.o DiscreteCostFunction.o  DiscreteModel.o
 Mylib=libdiscrete
 
 ifdef HOCR
@@ -18,26 +15,14 @@ ifdef HOCR
 endif
 
 ifdef GROUP
-	MYPROGRAMOBJ+= DiscreteGroupCostFunction.o  DiscreteGroupModel.o   
+	MYPROGRAMOBJ+= DiscreteGroupCostFunction.o  DiscreteGroupModel.o
 endif
 
 ifdef TBB
 	USRCXXFLAGS+= -DHAS_TBB
-	LIBS=-ltbb -lnewmeshclass -lfslsurface -lgiftiio  -lexpat -lfslvtkio -lnewimage  -lmiscmaths -lfslio -lniftiio -lnewmat -lutils  -lbint -lnewran -lprob -lznz -lz
 endif
-
-
-
-#-----------------------------------------------------------------		
-
-MYINCLUDES=
-
-MYLIBRARIES=
-
-#------------------------------------------------------------------------------
 
 all: ${MYlib}.a
 
 ${MYlib}.a: ${MYPROGRAMOBJ}
 	${AR} -r libdiscrete.a ${MYPROGRAMOBJ}
-
diff --git a/src/MSM/Makefile b/src/MSM/Makefile
@@ -1,77 +1,73 @@
-# $id: Makefile,v 1.1.1.1 2013/10/08 14:06:18 emmar Exp $
 include ${FSLCONFDIR}/default.mk
 
 PROJNAME= MSM
 USRCXXFLAGS=-g
-HOCR=True 
 
 USRINCFLAGS=-I${INC_NEWMAT} -I${INC_NEWRAN} -I${INC_ZLIB} -I${INC_CPROB} -I${INC_PROB}  -I${INC_GD}  -I${INC_GDC} -I${INC_PNG} -I${INC_BOOST} -I./include -I${FSLDEVDIR}/include -I${FSLDEVDIR}/extras/include
 USRLDFLAGS=-L${LIB_NEWMAT} -L${LIB_NEWRAN} -L${LIB_ZLIB}  -L${LIB_CPROB} -L${LIB_PROB} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_GD}   -L. -L${FSLDEVDIR}/lib  -L${FSLDEVDIR}/extras/lib
-LIBS= -lmeshreg -lfastpd -ldiscrete -lnewmeshclass -lfslsurface -lgiftiio -lmm  -lexpat  -lfslvtkio -lnewimage  -lmiscmaths -lmiscplot -lmiscpic -lfslio -lniftiio -lnewmat -lutils  -lbint -lnewran -lprob -lznz -lgdc -lgd -lpng  -lz
+LIBS= -lmeshreg -lfastpd -ldiscrete -lnewmeshclass -lfslsurface -lgiftiio -lmm -lexpat -lfslvtkio -lnewimage -lmiscmaths -lmiscplot -lmiscpic -lNewNifti -lutils  -lbint -lnewran -lprob -lznz -lgdc -lgd -lpng  -lz
 
 ifdef HOCR
 	USRCXXFLAGS+= -std=c++11  -DHAS_HOCR
 endif
 
 ifdef TBB
 	USRCXXFLAGS+= -DHAS_TBB
-	LIBS= -lmeshreg -lfastpd -ldiscrete -ltbb -lnewmeshclass -lfslsurface -lgiftiio -lmm  -lexpat  -lfslvtkio -lnewimage  -lmiscmaths -lmiscplot -lmiscpic -lfslio -lniftiio -lnewmat -lutils  -lbint -lnewran -lprob -lznz -lgdc -lgd -lpng  -lz
+	LIBS= -lmeshreg -lfastpd -ldiscrete -ltbb -lnewmeshclass -lfslsurface -lgiftiio -lmm -lexpat -lfslvtkio -lnewimage -lmiscmaths -lmiscplot -lmiscpic -lNewNifti -lutils  -lbint -lnewran -lprob -lznz -lgdc -lgd -lpng  -lz
 
 endif
 
 ifdef GROUP
 	all:= msm_group msm_metricmath msmresamplemesh  estimate_strains estimate_curvature msm_metric_average msm_makeicos intensity_normalise minimise_anat-to-sphere_distortions:
 endif
 
-all:msm  msmapplywarp  estimate_metric_distortion surfconvert msmresample msm_metric_sim 
+all:msm  msmapplywarp  estimate_metric_distortion surfconvert msmresample msm_metric_sim
 
 libmsm.a: ${MSMLIBOBJS}
 	${AR} -r libmsm.a ${MSMLIBOBJS}
 
 
 msm: msm.o
-	${CXX} ${LDFLAGS} -o $@ msm.o ${LIBS} 
+	${CXX} ${LDFLAGS} -o $@ msm.o ${LIBS}
 msm_group: msm_group.o
-	${CXX} ${LDFLAGS} -o $@ msm_group.o ${LIBS} 
+	${CXX} ${LDFLAGS} -o $@ msm_group.o ${LIBS}
 
 msm_makeicos: msm_makeicos.o
-	${CXX} ${LDFLAGS} -o $@ msm_makeicos.o ${LIBS} 
+	${CXX} ${LDFLAGS} -o $@ msm_makeicos.o ${LIBS}
 intensity_normalise: intensity_normalise.o
-	${CXX} ${LDFLAGS} -o $@ intensity_normalise.o ${LIBS} 
+	${CXX} ${LDFLAGS} -o $@ intensity_normalise.o ${LIBS}
 msm_metricmath: msm_metricmath.o
-	${CXX} ${LDFLAGS} -o $@ msm_metricmath.o ${LIBS} 
+	${CXX} ${LDFLAGS} -o $@ msm_metricmath.o ${LIBS}
 msm_surface_average: msm_surface_average.o
-	${CXX} ${LDFLAGS} -o $@ msm_surface_average.o ${LIBS} 
+	${CXX} ${LDFLAGS} -o $@ msm_surface_average.o ${LIBS}
 msm_metric_sim: msm_metric_sim.o
-	${CXX} ${LDFLAGS} -o $@ msm_metric_sim.o ${LIBS} 
+	${CXX} ${LDFLAGS} -o $@ msm_metric_sim.o ${LIBS}
 
 estimate_strains: estimate_strains.o
-	${CXX} ${LDFLAGS} -o $@ estimate_strains.o ${LIBS} 
+	${CXX} ${LDFLAGS} -o $@ estimate_strains.o ${LIBS}
 estimate_curvature: estimate_curvature.o
-	${CXX} ${LDFLAGS} -o $@ estimate_curvature.o ${LIBS} 
+	${CXX} ${LDFLAGS} -o $@ estimate_curvature.o ${LIBS}
 
 groupsegmentation: groupsegmentation.o
-	${CXX} ${LDFLAGS} -o $@ groupsegmentation.o ${LIBS} 
+	${CXX} ${LDFLAGS} -o $@ groupsegmentation.o ${LIBS}
 
 msmapplywarp: msmapplywarp.o
-	${CXX}  ${LDFLAGS} -o $@  msmapplywarp.o ${LIBS} 
+	${CXX}  ${LDFLAGS} -o $@  msmapplywarp.o ${LIBS}
 
 msmresample: msmresample.o
-	${CXX}  ${LDFLAGS} -o $@  msmresample.o ${LIBS} 
+	${CXX}  ${LDFLAGS} -o $@  msmresample.o ${LIBS}
 
 msmresamplemesh: msmresamplemesh.o
-	${CXX} ${LDFLAGS} -o $@ msmresamplemesh.o ${LIBS} 
+	${CXX} ${LDFLAGS} -o $@ msmresamplemesh.o ${LIBS}
 
 estimate_metric_distortion: estimate_metric_distortion.o
-	${CXX} ${LDFLAGS} -o $@ estimate_metric_distortion.o ${LIBS} 
+	${CXX} ${LDFLAGS} -o $@ estimate_metric_distortion.o ${LIBS}
 
 minimise_anat-to-sphere_distortions: minimise_anat-to-sphere_distortions.o
-	${CXX} ${LDFLAGS} -o $@ minimise_anat-to-sphere_distortions.o ${LIBS} 
+	${CXX} ${LDFLAGS} -o $@ minimise_anat-to-sphere_distortions.o ${LIBS}
 
 msm_metric_average: msm_metric_average.o
-	${CXX}  ${LDFLAGS} -o $@  msm_metric_average.o ${LIBS} 
+	${CXX}  ${LDFLAGS} -o $@  msm_metric_average.o ${LIBS}
 
 surfconvert: surfconvert.o
-	${CXX}  ${LDFLAGS} -o $@  surfconvert.o ${LIBS} 
-
-
+	${CXX}  ${LDFLAGS} -o $@  surfconvert.o ${LIBS}
diff --git a/src/MSMRegLib/Makefile b/src/MSMRegLib/Makefile
@@ -1,13 +1,10 @@
-# $id: Makefile,v 1.1.1.1 2013/10/08 14:06:18 emmar Exp $
 include ${FSLCONFDIR}/default.mk
 
 PROJNAME = MeshReg
-USRCXXFLAGS=-g 
-HOCR=True
+USRCXXFLAGS=-g
 
 USRINCFLAGS =-I${INC_NEWMAT} -I${INC_NEWRAN} -I${INC_ZLIB} -I${INC_CPROB} -I${INC_PROB}  -I${INC_GD}  -I${INC_GDC} -I${INC_PNG} -I${INC_BOOST} -I${FSLDEVDIR}/include -I${FSLDEVDIR}/extras/include
 USRLDFLAGS =-L${LIB_NEWMAT} -L${LIB_NEWRAN} -L${LIB_ZLIB}  -L${LIB_CPROB} -L${LIB_PROB} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_GD}   -L. -L${FSLDEVDIR}/lib  -L${FSLDEVDIR}/extras/lib
-LIBS= -lmsm -lfastpd -ldiscrete -lnewmeshclass -lfslsurface -lgiftiio -lmm  -lexpat  -lfslvtkio -lnewimage  -lmiscmaths -lmiscplot -lmiscpic -lfslio -lniftiio -lnewmat -lutils  -lbint -lnewran -lprob -lznz -lgdc -lgd -lpng  -lz
 MSMLIBOBJS= ContinuosOpt.o meshmodify.o meshreg.o
 
 ifdef HOCR
@@ -16,20 +13,17 @@ ifdef HOCR
 endif
 
 ifdef GROUP
-	MSMLIBOBJS+= groupmeshreg.o   	
+	MSMLIBOBJS+= groupmeshreg.o
 endif
 
 ifdef TBB
 	USRCXXFLAGS+= -DHAS_TBB
-	LIBS= -lmsm -lfastpd -ldiscrete -ltbb  -lANN -lnewmeshclass -lfslsurface -lgiftiio -lmm  -lexpat -lfirst_lib -lshapeModel -lfslvtkio -lmeshclass -lnewimage  -lmiscmaths -lmiscplot -lmiscpic -lfslio -lniftiio -lnewmat -lutils  -lbint -lnewran -lprob -lznz -lgdc -lgd -lpng  -lz
-endif 
+endif
 
 
 
 
-all: libmeshreg.a 
+all: libmeshreg.a
 
 libmeshreg.a: ${MSMLIBOBJS}
 	${AR} -r libmeshreg.a ${MSMLIBOBJS}
-
-